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Windows 7: Windows will not boot - even after factory reset

I had been having problems with my work PC for months. Very slow boot up, lagging during use, programs not responding etc...
Then worse issues started like the system restore not saving any restore points, not allowing me to manually create restore points...

I tried all the normal stuff.

Sfc Scan came up clean, Check disk came up clean, AVG and Malwarebytes scans were clean....

It seemed like the longer I left it on the better it ran, but anytime it restarted it got terrible again. Then about a week ago I tried to do another Check Disk, I scheduled it and restarted the PC as I was leaving for the day.
When I got in the next morning I checked the event log and no Check disk was on there. So I tried it again that day and the same thing happened.

Then yesterday it all blew up. I was on my PC it was mostly running ok, except for skype which would not properly connect. Since I need that program working to do my job I restarted the PC.

It would let me enter my password but then was stuck on the Welcome screen for about 30 minutes.
So I powered down and tried to boot into safe mode, and it did the same thing, stuck on the welcome screen.
So I powered down again and went into start up repair. Startup repair failed.

I used a command prompt to run check disk on C: and it only took about 30 seconds which I found odd but it said it came up clean. I also did it on DBackup) and it also took about 30 seconds and came up clean. Then I did it on EOS) and it was going extremely slow. Even the first verification stage it was average 3 minutes to scan each file. At this point I had just left it there to work on itself while I did other things in the office and when I came back to the PC it had just powered itself down. I dont know if it ever finished the scan.

So at this point I couldn't waste any more time on this and all my files and programs were backed up externally so I just did a factory reset.

Which seemed to work. Yesterday afternoon everything was running smoothly and quickly.

This morning I come in and try to log in - once again frozen on the welcome screen. After about 30 minutes I tried to reboot and was forced back into the startup repair.

Where can I possibly go from here? If a fresh install didn't work then what will?

Recently I had a Hard Drive go bad and all it would do is stop at the Windows Logo. I put in another HDD with Windows on it and things worked fine. If you have another HDD, you might try that to determine if it is a bad HDD.

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